comparison MetaProSIP.xml @ 1:a25d96e0d837 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14

0:f0e3cb65a6bd

<?xml version='1.0' encoding='UTF-8'?>
<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
<!--Proposed Tool Section: [Utilities]-->
<tool id="MetaProSIP" name="MetaProSIP" version="2.1.0">
  <description>Performs proteinSIP on peptide features for elemental flux analysis.</description>
  <macros>
    <token name="@EXECUTABLE@">MetaProSIP</token>
    <import>macros.xml</import>
  </macros>

#end if
#if $param_weight_merge_window:
  -weight_merge_window $param_weight_merge_window
#end if
#if $param_plot_extension:
  -plot_extension $param_plot_extension
#end if
#if $param_qc_output_directory:
  -qc_output_directory     "$param_qc_output_directory"
#end if
#if $param_labeling_element:
  -labeling_element $param_labeling_element
#end if
#if $param_use_unassigned_ids:
  -use_unassigned_ids
#end if
#if $param_use_averagine_ids:

#end if
    #if $adv_opts.param_score_plot_yaxis_min:
  -score_plot_yaxis_min $adv_opts.param_score_plot_yaxis_min
#end if
    #if $adv_opts.param_collect_method:
  -collect_method $adv_opts.param_collect_method
#end if
    #if $adv_opts.param_lowRIA_correlation_threshold:
  -lowRIA_correlation_threshold $adv_opts.param_lowRIA_correlation_threshold
#end if
    #if $adv_opts.param_force:

</command>
  <inputs>
    <param name="param_in_mzML" type="data" format="mzml" optional="False" label="Centroided MS1 data" help="(-in_mzML) "/>
    <param name="param_in_fasta" type="data" format="fasta" optional="False" label="Protein sequence database" help="(-in_fasta) "/>
    <param name="param_in_featureXML" type="data" format="featurexml" optional="False" label="Feature data annotated with identifications (IDMapper)" help="(-in_featureXML) "/>
    <param name="param_r_executable" type="data" format="text" value="R" label="Path to the R executable (default: 'R')" help="(-r_executable) "/>
    <param name="param_mz_tolerance_ppm" type="float" value="10.0" label="Tolerance in ppm" help="(-mz_tolerance_ppm) "/>
    <param name="param_rt_tolerance_s" type="float" value="30.0" label="Rolerance window around feature rt for XIC extraction" help="(-rt_tolerance_s) "/>
    <param name="param_intensity_threshold" type="float" value="10.0" label="Intensity threshold to collect peaks in the MS1 spectrum" help="(-intensity_threshold) "/>
    <param name="param_correlation_threshold" type="float" value="0.7" label="Correlation threshold for reporting a RIA" help="(-correlation_threshold) "/>
    <param name="param_xic_threshold" type="float" value="0.7" label="Minimum correlation to mono-isotopic peak for retaining a higher isotopic peak" help="(-xic_threshold) If featureXML from reference file is used it should be disabled (set to -1) as no mono-isotopic peak is expected to be present"/>

    <data name="param_out_peptide_centric_csv" format="tabular"/>
  </outputs>
  <help>Performs proteinSIP on peptide features for elemental flux analysis.


For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/doxygen/parameters/output/UTILS_MetaProSIP.html</help>
</tool>

1:a25d96e0d837

<?xml version='1.0' encoding='UTF-8'?>
<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
<!--Proposed Tool Section: [Utilities]-->
<tool id="MetaProSIP" name="MetaProSIP" version="2.2.0.1">
  <description>Performs proteinSIP on peptide features for elemental flux analysis.</description>
  <macros>
    <token name="@EXECUTABLE@">MetaProSIP</token>
    <import>macros.xml</import>
  </macros>

#end if
#if $param_weight_merge_window:
  -weight_merge_window $param_weight_merge_window
#end if
#if $param_plot_extension:
  -plot_extension
  #if " " in str($param_plot_extension):
    "$param_plot_extension"
  #else
    $param_plot_extension
  #end if
#end if
#if $param_qc_output_directory:
  -qc_output_directory     "$param_qc_output_directory"
#end if
#if $param_labeling_element:
  -labeling_element
  #if " " in str($param_labeling_element):
    "$param_labeling_element"
  #else
    $param_labeling_element
  #end if
#end if
#if $param_use_unassigned_ids:
  -use_unassigned_ids
#end if
#if $param_use_averagine_ids:

#end if
    #if $adv_opts.param_score_plot_yaxis_min:
  -score_plot_yaxis_min $adv_opts.param_score_plot_yaxis_min
#end if
    #if $adv_opts.param_collect_method:
  -collect_method
  #if " " in str($adv_opts.param_collect_method):
    "$adv_opts.param_collect_method"
  #else
    $adv_opts.param_collect_method
  #end if
#end if
    #if $adv_opts.param_lowRIA_correlation_threshold:
  -lowRIA_correlation_threshold $adv_opts.param_lowRIA_correlation_threshold
#end if
    #if $adv_opts.param_force:

</command>
  <inputs>
    <param name="param_in_mzML" type="data" format="mzml" optional="False" label="Centroided MS1 data" help="(-in_mzML) "/>
    <param name="param_in_fasta" type="data" format="fasta" optional="False" label="Protein sequence database" help="(-in_fasta) "/>
    <param name="param_in_featureXML" type="data" format="featurexml" optional="False" label="Feature data annotated with identifications (IDMapper)" help="(-in_featureXML) "/>
    <param name="param_r_executable" type="data" format="txt" value="R" label="Path to the R executable (default: 'R')" help="(-r_executable) "/>
    <param name="param_mz_tolerance_ppm" type="float" value="10.0" label="Tolerance in ppm" help="(-mz_tolerance_ppm) "/>
    <param name="param_rt_tolerance_s" type="float" value="30.0" label="Rolerance window around feature rt for XIC extraction" help="(-rt_tolerance_s) "/>
    <param name="param_intensity_threshold" type="float" value="10.0" label="Intensity threshold to collect peaks in the MS1 spectrum" help="(-intensity_threshold) "/>
    <param name="param_correlation_threshold" type="float" value="0.7" label="Correlation threshold for reporting a RIA" help="(-correlation_threshold) "/>
    <param name="param_xic_threshold" type="float" value="0.7" label="Minimum correlation to mono-isotopic peak for retaining a higher isotopic peak" help="(-xic_threshold) If featureXML from reference file is used it should be disabled (set to -1) as no mono-isotopic peak is expected to be present"/>

    <data name="param_out_peptide_centric_csv" format="tabular"/>
  </outputs>
  <help>Performs proteinSIP on peptide features for elemental flux analysis.


For more information, visit http://www.openms.de/comp/metaprosip/</help>
</tool>